[Biojava-dev] Smith-Waterman algorithm

[Schreiber, Mark]

Hi -

The biojava dp package include HMM stuff which can be used to perform
pairwise alignments. However, this is possibly slower (although more
sensitive) than SW and NW. I think it would be good to get the two
algorithms into to the package simply because they are so familiar and
widely used in bioinformatics.

- Mark

> -----Original Message-----
> From: jim.donohoe@earthlink.net [mailto:jim.donohoe@earthlink.net] 
> Sent: Tuesday, 19 November 2002 11:03 a.m.
> To: biojava-dev@biojava.org
> Subject: [Biojava-dev] Smith-Waterman algorithm
> 
> 
> Biojava developers:
> 
> Is anyone currently developing a sequence matcher using the 
> Smith-Waterman algorithm?  I wrote a quick and dirty 
> implementation for an assignment in a bioinformatics course 
> (University California Santa Cruz, Extension), and I'm 
> considering developing an industrial-strength version as a 
> course project over the next few weeks.
> 
> I'm not yet familiar with the biojava architecture, and at 
> this point I'm just a beginner in biology, but I have a 
> decent background in math and CSci and several years of 
> full-time Java experience.
> 
> My project would include:
> 	
> 	Use of the biojava architecture
> 
> 	Needleman-Wunsch & Smith-Waterman algorithms
> 
> 	Support for multi-threading
> 
> 	Return multiple results, scored and sorted
> 	
> Please let me know if this sounds useful, or if you have any 
> other suggestions--regarding this proposal or perhaps some 
> other project--I'd like 
> to hear them.
> 
> Thanks for your time,
> 
> Jim Donohoe
> 505 Cypress Point Drive #285
> Mountain View, CA 94043
> 650-964-1193
> jim.donohoe@computer.org
> 
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> biojava-dev mailing list
> biojava-dev@biojava.org 
> http://biojava.org/mailman/listinfo/biojava-dev
> 
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